I don't see any reason to do a transmitter calibration. There should be no need to do ANY calibration on a new quad! And there is no need to automatically update the firmware. FWIW, mine came with the newest firmware and I bought it last spring.
Things that SHOULD be done to a new quad:
Change the limits to something reasonable. 2,000 yards is a ridiculous limit. Beginners should set these pretty low, so the quad doesn't get so far away they lose orientation.
Make sure the motor cutoff is set on intelligent and not immediate. The NAZA manual says he default is immediate.
Turn on IOC. Home Lock is a life saver when it gets far away and you don't know which way it is pointing.
Set the bottom position on S1 to Failsafe. It is set to ATTI, just like the center position, by default.
To start the motors, many combinations of the stick placements will work. Both in lower left, both in lower right, both in lower corners close to each other and both on opposite lower corners.
And doing any of these will also shut off the motors, even while in flight